Sync presets just configure the panel, the actual operation is exactly the same - so can you see any difference between the preset and how you're configuring it manually?
However further testing is showing it seems to be an issue when dealing with sub-folders. And I've made it not work with a non-saved one as well now. It was just my testing started there, it didn't work, so I set one up manually, and then it did...but that's not the root cause it seems.
If I narrow the sync, by going in to the sub-folder with change, on both sides, & running 'Compare' it then works (saved sync or not), with all other settings the same.
I do have 'Sync sub-folder contents' ticked (in both cases).
Without more information about how you've configured the panel and the folders involved it's hard to know what to suggest.
You can turn on Preferences / Miscellaneous / Advanced: [Troubleshooting] sync_debug if you like, that will write a log file on your desktop showing all the comparisons and the results. Might shed some light on what's going on.
Very quick test of the new beta - not fixed as far as I can tell.
Have to head in to work, but can look into it more tonight. But first test found no changes as with the previous beta, and there are definitely changes...